Ch. 9: Intro to microbial genetics Flashcards
Genome
complete set of chromosomes and genes in an organism; plasmids
sum total of all genetic information of cell; DNA divided up into Genes
plasmid
extrachromosomal genetic unit characterized by several features; double-stranded DNA that is smaller than and replicates independently of cell chromosome; bears gene not essential for cell growth; transmissible to other bacteria
genes
site on a chromosome that provides information for a certain cell function; specific DNA segment that necessary code to make protein/ RNA molecule
fundamental unit of heredity that provides a trait to an organism; sections/sequences of DNA within DNA strand
genotype
the genetic makeup of an organism as inherited from parents; responsible for phenotype or expressed characteristics
what types of genes an organism contains; alleles
phenotype
observable characteristics of an organism produced by expression of its genetic potential (Genotype); includes morphological and physiological traits
physical traits/ what does the organism look like?
histones
protein associated with eukaryotic DNA; serve as scaffolding to compact and condense DNA into chromosomes; also enhance or prevent expression of certain genes
nucleosomes
structure in the packaging of eukaryotic DNA formed when the DNA strands wrap around histone proteins, forming an arrangement that looks like beads on a chain
semi-conservative replication
in DNA replication, during synthesis of new DNA strands (the daughter DNA) the parent strand template DNA is retained in the final molecule
produce two copies that each contained one of the original strands of DNA and one new strand. Semiconservative replication is beneficial to DNA repair.
DNA replication
the biological process of producing two identical replicas of DNA from one original DNA molecule.
-DNA replication occurs in all living organisms acting as the most essential part of biological inheritance.
transcription
definition + steps
the process by which a strand of RNA is produced against a DNA template
taking DNA molecule and copying one of its strands into an RNA molecule; if it is mRNA, can be used to make protein
Initiation- RNA polymerase binds to A-T rich region;;; DNA sequence called promoter region; promoter is 5 prime 2; before coding region of gene;;; opens double helix to reveal info inside
—for prokaryotes, RNA polymerase binds by sigma factor, but in euk, determined by variety of factors (diff locations for euks.)
Elongation- RNA polymerase moves along the DNA strand; nucleotides added 1 by 1 based on what complements to DNA template strand to make a long RNA strand; double helix coils and reforms behind RNA polymerase as it moves
Termination sequence- RNA polymerase recognizes a termination site> causes molecular distortion causing RNA polymerase to fall of DNA molecule, releasing RNA molecule, and RNA polymerase can be used again to transcribe
Codon
a sequence of 3 nucleotides in mRNA
-translated into a single amino acid
coding strand
the coding strand is the DNA strand whose base sequence is identical to the base sequence of the RNA transcript produced.
-this strand contains codons, while the non-coding strand contains anticodons.
introns
(eukaryotes only)
a contracted version of “intragenic regions”
Segments on split genes of eukaryotes that do not code for polypeptide; serve other functions
[[[intervening stretches of DNA that are not expressed are called introns]
During transcription, exons are separated from introns and spliced together into a continuous mRNA transcript]]]
exons
(eukaryotes only)
a section of eukaryotic DNA coding for a corresponding portion of mRNA that is translated into proteins
[intervening stretches of DNA that are not expressed are called introns]
During transcription & translation, exons are separated from introns and spliced together into a continuous mRNA transcript
operon
(only in prok/bacteria)
set of more than one gene that makes a single mRNA molecule; regulated together; transcription on or off so genes are all on/expressed or off.
inducible- turn on/increase gene expression (default is off)
OR
repressible- default on, can be shut off
mutations
a permanent inheritable alteration in the DNA sequence or content of a cell
wild-type
the natural, non mutated form of a genetic trait
Epigenetics
study of how cells control gene activity without changing the DNA sequence
study of changes above/beyond nucleotide changes
conjugation
in bacteria, contact between donor and recipient cells associated with transfer of genetic material like plasmids ; can involve special (sex) pili; also form of sexual recombination in ciliated protozoans
transformation
microbial genetics: transfer of genetic material contained in “naked” DNA fragments from a donor cell to a competent recipient cell
transduction
transfer of genetic material from one bacterium to another by means of a bacteriophage vector; accidental
transposons
DNA segment with an insertion sequence at each end, enabling it to migrate to another plasmid, to the bacterial chromosome, or to a bacteriophage
happens in all organisms including our cells… individual DNA pieces that move around on their own inside our cells (some can replicate) they are single, jumping genes. Can move from 1 location to another, sometimes copy themselves, or escape and leave cell… = Mutation or change in DNA = genetic evolution
supercoiling is how:
prokaryotes package DNA
The first enzyme used in DNA replication is:
Gyrase [uncoiling supercoil, to loosen helix]
genetics
study of inheritance; understanding trait a cell gets from parent(s)
Structural Gene
any gene that codes for protein; mRNA translated to make protein
Regulatory genes
just regulate/control other genes; controlling gene expression
around how many genes are in the human genome?
In E coli?
Human- 21,000
Ecoli- around 4,000 [4,288]
what is a nucleotide made of
pentose sugar, nitrogenous base, phosphate group
in the backbone of DNA what kind of bond is it between the phosphate and sugar?
phosphodiester bond
how does phosphate affect the DNA?
makes it negatively charged
Structural genes code for:
cellular proteins.
Eukaryotic chromosomes differ from prokaryotic chromosomes because only eukaryotes have
-elongated linear, not circular, chromosomes.
-several to many chromosomes.
-histone proteins.
-chromosomes in a nucleus.
Among the microorganisms, various genomes can include
plasmids.
chromosomes.
mitochondrial DNA.
chloroplast DNA.
The expression of genetic traits is the
phenotype
The ________ is all of the genetic material of a cell.
genome
A nucleosome is a linear chromosome wound around the:
histone
DNA gyrase function
supercoils DNA.
Okazaki fragments are attached to each other to form a continuous lagging strand by the enzyme:
DNA ligase.
Helicase function
unzips DNA.
DNA polymerase III function
synthesizes new DNA only in the 5’ to 3’ direction.
adding bases to the new DNA chain, proofreading the chain for mistakes
The enzyme that helps pack DNA into the cell by coiling the DNA into a tight bundle is
DNA gyrase.
The duplication of a cell’s DNA is called
replication.
Telomeres are found:
at the ends of linear DNA
for Euk.s, transcription occurs in the:
Translation occurs in the:
nucleus or at the nucleoid.
Cytoplasm or attached to rough ER
During translation elongation, the next tRNA enters into the:
A site
Transcription
process of ______?
Occurs in _______
requires a ___________ strand
requires __________ polymerase
Occurs before ____________
is a process of RNA synthesis.
Occurs in nucleus/nucleoid
requires a template DNA strand [[[strand being copied]]]
requires RNA polymerase.
occurs before translation.
RNA molecules differ from DNA molecules because only RNA
is typically one strand of nucleotides.
does not have thymine.
has ribose.
has uracil.
A sequence of nucleotides in the eukaryotic gene that is transcribed but removed prior to translation is a/an:
intron.
The three-base sequence on mRNA that codes for an amino acid is called a(n)
codon.
Groups of three consecutive bases along the DNA of a gene have the code for one
amino acid
Synthesis of the lac operon enzymes requires
lactose binding to the repressor.
The induced mutation is a mutation that arises from:
exposure of an organism’s DNA to a mutagen. Tautomers, physical or chemical mutagens may cause it. Mutagens can insert, delete or substitute a nucleotide.
A screening system called the ________ test is used for detecting chemicals with carcinogenic potential.
Ames
A frameshift is caused by ________ mutations?
deletion and insertion
Name the 3 types of bacterial DNA recombination
conjugation
transduction
transformation
The transfer of DNA fragments from a dead cell to a live, competent recipient cell that results in a changed recipient cell is
transformation.
The development of virulent, toxin-producing bacterial strains due to the activity of a bacteriophage occurs in
transduction.
Base pairs in DNA are held together by ________ bonds.
hydrogen
DNA is made up of subunits called
nucleotides
The antiparallel arrangement within DNA molecules refers to
one helix strand that runs from the 5’ to 3’ direction and the other strand runs from the 3’ to 5’ direction.
The smallest unit of heredity is:
gene
Replication of DNA begins at a(n)
AT rich area.
at the origin of replication
Histones are used in:
eukaryotes
DNA polymerase I function
removes RNA primers.
Gene regulation can involve a repressor that blocks ________ from initiating transcription.
RNA polymerase
A mutation that changes a normal codon to a stop codon is called a
nonsense mutation.
Bacterial conjugation involves
a donor cell that transfers a copy of a plasmid to a recipient cell through a pilus.
What are 3 types of RNA involved in translation?
Messenger mRNA- the only RNA molecule that carries info to be translated/ to make a protein; length varies greatly; carries codons
Tools:
ribosomal rRNA- part protein part RNA
transfer tRNA- Transferring single amino acid to form the protein
Sense strand
strand that makes sense; cell uses this to make protein product
what is the name of the sequence where transcription starts?
promoter
what happens in the A site in the ribosome?
new tRNA enters
where/when does DNA replication start and end?
start at the origin (of replication)
ends when all DNA is copied
what enzyme copies DNA in replication?
mainly DNA polymerase III (Also I)
Where does transcription start/end?
Which enzyme is responsible?
starts with- promoter sequence
ends- termination sequence
enzyme responsible- RNA polymerase
Where does translation start/end?
what enzyme complex is responsible for translation?
starts at the start codon (AUG)
ends at stop codons (UAA, UGA..)
enzyme responsible- ribosome
What is the most commonly used technique by genetic engineers?
transformation
chromosomes in prokaryotes VS eukaryotes VS viruses
prok- circular; 1 copy usually- haploid
euk- linear- pairs; diploid
virus- either DNA OR RNA; very small; only genes required for replication (host will provide stuff they need)
what are the 3 types of genes?
structural genes [code for proteins]
regulatory genes [just sit as an important genetic sequence; control gene expression]
“genes” no specific name [code for RNA…like ribosomal rRNA or genes used to make tRNA; not proteins]
Chromosome:
All DNA that is required for life
DNA charge VS DNA polarity
Phosphate determines charge of DNA
Sugar gives polarity; how it is formed
Name the six enzymes involved in DNA replication and describe, in order, what their roles are
Gyrase: uncoiling supercoil + supercoiling
Helicase: unzipping the DNA helix
Primase: synthesizing an RNA primer
DNA Polymerase III: adding bases to the new DNA chain, proofreading the chain for mistakes
DNA polymerase I: removing RNA primers, replacing gaps between Okazaki fragments with correct nucleotides, repairing mismatched bases
Ligase: final binding of nicks in DNA during synthesis; phosphodiester bonds
difference between ribosome VS ribozyme
Ribozyme- special, single enzyme made of rRNA; catalysts; part of ribosome;
Ribosome- enzymatic complex; lots of parts
Describe how operons are regulated using Lac Operon
inducible operon- only turned on with lactose (sugar)— lactose operon found in E.coli cells
-requires 3 DNA regions
—Repressor gene- makes repressor protein [allosteric molecule] involved in regulating lac operon.
—control locus- involves 2 regulatory genes - promoter gene & operator [don’t make product, but regulate the structural genes in operon]
—structural locus- where structural genes 1-2-3 are to make enzymes to digest/transport/use lactose.
—-2 scenarios—
- operon off- no lactose
-repressor protein has to bind to the operator sequence on DNA strand and block RNA polymerase from moving [cannot transcribe, no mRNA or enzymes produced] - operon on- lactose present
-repressor protein binds lactose [fall off operator] binds to promoter and transcribes structural locus> forms single mRNA strand with 3 separate structural genes with their own start/stop codons & shine-delgarno sequences> 3 proteins repeatedly formed to digest lactose; once all lactose is consumed/used in microbial metabolism, shuts down lac operon expression 1 more time; back in default state
name the types of point mutations
wild-type [non-mutated; normal]
substitution [missense or nonsense]
inversion
frameshift [insertion or deletion]
reverse
silent
which mutation has the worst effect on an organism? Which has no effect?
worst- frameshift & nonsense
no effect- silent
wild-type gene
(nonmutated) sequence [normal sequence found in most organisms]
[THE BIG BAD CAT ATE THE FAT RED CAT]
Substitution mutation
A) Missense- usually, tolerated and fine.. 1 nucleotide change/ Small change; may or may not make a huge impact on protein =
[THE BIG MAD CAT ATE THE FAT RED BUG]
B) Nonsense- converts codon to stop codon; premature termination of protein synthesis; usually severe effect;
[THE BIG BAD XXX (STOP)]
Inversion mutation
adjacent letters exchange places; can result in significant changes
Frameshift mutation
extreme effects; every amino acid after this is very impacted
A) Insertion- addition of letter
B) Deletion- deletion of letter
Reverse mutation
happens in mutants that change the mutated sequence back to wild-type state; reverting to protein’s original function
Silent mutation
change in nucleotide from one to another nucleotide that does not affect the primary amino acid sequence— no significant negative effect
Spontaneous Vs induced mutations
Spontaneous- randomly happen, can’t prevent
Induced- caused by environmental factors; smoking, chemicals, UV light from sun, from nuclear power plants..processed meats, burnt toast, asbestos.. Peanutbutter, alcohol
Ames test
Take a set of mutant bacteria; look for reverse mutations; these mutant bacteria cannot grow on a certain type of medium, if you plate them here they should be dead, aside from spontaneous mutations, colonies will grow = mutants
-also for detecting chemicals with carcinogenic potential.
Describe four methods other than sexual reproduction whereby organisms recombine their genetic sequences.
Conjugation- using protein bridge (pilus); sending a plasmid from one cell to another; plasmids are advantageous genes ex) metal resistance, toxin/enzyme production, iron uptake…
Transformation- done by competent cells; taking/absorbing naked DNA from any source and trying it out; most cells are not naturally competent.
Transduction- virus carried DNA pieces; a bacteriophage viral particle infects certain host cell>accidental introduction of some of host cell chromosome to bacteriophage
Transposons- [[[mixing DNA within a single cell]]] happen in all organisms including our cells… individual DNA pieces that move around on their own inside our cells (some can replicate) they are single, jumping genes. Can from 1 location to another, sometimes copy themselves, or escape and leave cell… = Mutation or change in DNA = genetic evolution
chromatin
DNA bound by histone proteins in eukaryotic cells
-could be loosely (when DNA found in typical cell not going thru cell divison) or very tightly wrapped
-highly compact chromatin (condensed chromatin) only when cell getting ready to divide; half DNA to each side of cell so daughter cells receive exact copy of DNA
how do prokaryotes VS eukaryotes package DNA?
prokaryotes- DNA gyrase; supercoiling
eukaryotes- histones
double helix can only grow on which end?
3 prime end (not 5)
when double helix is opened, ______ bonds are broken
hydrogen
in order to synthesize DNA, there already must exist a :
nucleic acid strand, already there, intact, then you can add DNA nucleotides to it
is DNA or RNA more stable?
DNA
[RNA is unstable, can mutate rapidly]
primase function
synthesizing RNA primer
-adds RNA nucleotides 1 by 1 until it has a short RNA strand (RNA primer) starts DNA strand synthesis; u can add DNA to this RNA primer… (starting molecule)
how many bonds are A-T and G-C connected by?
A-T - connected by 2 hydrogen bonds (so easier for cell to pull these apart at the ori/origin of replication)
G-C - connected by 3 hydrogen bonds
replication bubble
open space between 2 single strand DNA molecules
-has 2 replication forks
-each fork has its own set of replication enzymes
Okazaki fragments
-associated with lagging strand
-part DNA and part RNA (newly synthesized lagging strands) will be connected by ligase eventually.
ligase function
replaces nicks
-all it does is forms a covalent bond (phosphodiester bond) between the DNA strands to make it 1 long continuous strand
-important for lagging strand synthesis- to connect chunks
Difference in DNA replication for Eukaryotes
similar to prokaryote DNA replication
-use same types on enzymes, but problem is euk. have much more DNA to copy…
-in order to copy DNA efficiently, one solution is to use multiple origins of replication in DNA strand
-Also, DNA is linear; telomeres on the end
what is the start codon and the amino acid?
[[[translation]]]
AUG
Euk: Methionine or MET
but in prokaryotes, it is formal methionine / fMET
what are the stop codons?
UAA
UAG
UGA
[not associated with any amino acids]
every single protein made on this planet has started with __________
methionine or formal methionine
_____________is unique because it is the only amino acid specified by a single codon.
Tryptophan
RNA
ribonucleic acid
full ribose sugar molecule attached to phosphate group and nitrogenous base
-single-stranded; but can fold on itself and form secondary/tertiary structures
secondary- hydrogen bonds
tertiary- hydrogen and other types of bonds
-URACIL instead of thymine; still binds with adenine in molecule formation
in transcription, what is the template strand?
what is the non-template strand?
template strand= the strand of DNA being copied
[product strand complements the template strand]
non-template strand is opposite of template DNA, not touched;;; but if mRNA being made, this could be referred to as the coding strand as it contains codon sequence
DNA VS RNA bases
DNA — AT CG
RNA — AU CG
spliceosomes
(eukaryotes only)
(euk)- enzyme complex used to cut out introns after transcription, before translation
excision repair
3 steps
most common mechanism for mutation repair
1) mutation identified and cut out by enzyme
2) DNA polymerase I replace newly missing nucleotides
3) Ligase brings it together
do most mutations have an effect?
no, but if they do have an effect, it is usually negative…
Rare positive effects- foundation of evolutionary change
Translation
5 steps
s of different gene types in single mRNA strand
protein synthesis; process of decoding a messenger RNA code into a polypeptide
Initiation- free mRNA floating in cytoplasm > small ribosomal subunit (30s in prok.) binds to shine-delgarno sequence found throughout the prok. mRNA.; several recipes/genes
—in EUK, the 40S subunit binds to 5 prime cap (beginning molecule of mRNA)
— initiator tRNA carries met or fMET to (& will bind to) start codon AUG in mRNA molecule via its anti codon in tRNA molecule
— large ribosomal subunit binds (50S or 60S prok/euk) > contains enzyme ribozyme (rRNA catalyst)»_space;> assembled ribosome has tRNA binding sites: A, P, E
A=amino site
P= peptide site
E= exit site [tRNAS leave here after dropping off amino acids]
Elongation- begins with initiator tRNA in P site, empty A and E site.
-Next tRNA with anticodon enters A site. Amino acid on tRNA in P site is removed & transferred to amino acid covalently bound to tRNA in A site. [peptide bond formation that ribozyme is responsible for]> mRNA pulled thru ribosome (by 3 nucleotides or 1 codon) this is called translocation. (tRNA will move from A > P > E site and exit.) Process will continue until hits stop codon.
Termination [site]- ribosome reaches a stop codon in the A site
Protein folding- this happens during elongation; as protein is being made; folds as it is being synthesized
Protein processing- changing protein shape/nature to make it function- such as by adding functional groups to make enzymes function better, or adding a cofactor like metal ions/vitamins [in case of insulin, needs to be cut and pieces removed to be functional]
euk- 1
prok- often more than 1
be able to draw picture of DNA replication
Draw a replication fork
Draw translation [both for Prok. and Euk]
prok. example pictured here
